(Q111442298)

English

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

scientific article published on 01 March 2021

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scholarly article

1 reference

10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing (English)

1 reference

10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

Gordon G Simpson

4

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10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

author name string

Matthew T. Parker

1

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10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

Katarzyna Knop

2

1 reference

10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

Geoffrey J. Barton

3

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31 March 2022

publication date

1 March 2021

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31 March 2022

1 reference

10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

22

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10.1186/S13059-021-02296-0

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31 March 2022

1

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31 March 2022

describes a project that uses

machine learning

1 reference

based on heuristic

inferred from title

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.

1 reference

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Evaluation and comparison of computational tools for RNA-seq isoform quantification

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Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro

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Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings.

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Nanopore native RNA sequencing of a human poly(A) transcriptome

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The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana

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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and mA modification

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2 April 2022

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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

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BEDTools: a flexible suite of utilities for comparing genomic features

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Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

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Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.

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A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Highly parallel direct RNA sequencing on an array of nanopores.

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A handful of intron-containing genes produces the lion's share of yeast mRNA.

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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

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deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index

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Comprehensive splice-site analysis using comparative genomics

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Transcriptome assembly from long-read RNA-seq alignments with StringTie2

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Identification of common molecular subsequences

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Identifiers

10.1186/S13059-021-02296-0

1 reference

10.1186/S13059-021-02296-0

https://api.crossref.org/v1/works/http://dx.doi.org/10.1186/s13059-021-02296-0

31 March 2022

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